Continue The War
by that bloke
Summary: The Crucible failed, the Catalyst decided extinction was best, and Shepard escapes Earth with the rest of the Fleet. What next?
1. Chapter 1

_**Prologue**_

_**Citadel:**_

"The paths are open. But you have to choose" The Catalyst said to a bleeding Commander Shepard. He thought about everything the AI had told him and the options it had presented. Destroy. Control. Synthesis. He had almost reached a decision and stepped forward.

"Shepard!" a voice buzzed over his earpiece.

"EDI? What are you doing here?" Shepard asked, wondering what she could be after right now.

"I've been listening to your conversation with the Catalyst AI. I have also been monitoring the Crucible from the Normandy. Shepard, the Catalyst is lying, the three options are a ruse to get rid of you!" she said

"Do not believe your construct, Shepard" the Catalyst replied, "it merely fears the Crucible's power. Now make your decision, human"

Shepard was suddenly unsure about the Catalysts intentions. But at the same time, he couldnt just abandon the Crucible after everything they had been through to get it here.

"Shepard, the Catalyst has taken control of the Crucible! you activate it and nothing will happen!" EDI responded through the comm.

He looked up at the Crucible, the various lights on the enormous machine were flickering. He pointed his gun at the image of the child.

"Why?" was his only word.

"Survival" it replied, but in a much deeper, booming voice reminiscent of a Reaper, "You would have destroyed us, we cannot allow that to happen."

"You bastard! I could have picked synthesis!"

"Synthesis is too unpredictable, even for us. You would never have chosen that when a chance for ultimate victory stood next to it. This Cycle has revealed that organics are too dangerous to evolve even this far. I have already devised a new, permanent solution"

"And that is?" Shepard asked

"Extermination" it retorted

"EDI, get me out of here!" Shepard barked into the comm.

"Roger that, commander"

"Shepard, be ready, we're coming in hot!" a familiar vooice radioed in

"Cortez? where?" Shepard looked up at the battle raging above

"You'll see me, I got a new shuttle!" and with that he flew in full-throttle, hitting the deck and skidding to a halt metres from Shepard. The doors opened and James and Ashley stepped out, fully armoured and carrying assault rifles.

"You look like shit, Loco!" James said

"Shepard, inside, quick!" Ash yelled as James held the Commander for support

Shepard limped into the shuttle as the Catalyst had a final thing to say

"Shepard" it said, causing James and Ash to point their rifles at it. "Regroup. Reload. Prepare. Wait. Fight. We will find you, your worlds, your armies, your children. We will show no mercy. No remorse. No regret. We will destroy you all."

Shepard only had one thing to say to this machine: "Fucking try it." The doors closed and the shuttle lifted away. As they cleared the Citadel Shepard looked out the window to see Reapers converging on the Crucible and opening fire, destroying months of resources and work.

"All Fleets, this is Admiral Hackett, abort the mission, I repeat, abandon Earth. We failed. Head through the Sol relay and scatter. Initiate Silent Contingency and await radio silence until further notice. We'll regroup, people. We'll beat them somehow. We'll continue the war..."


	2. Chapter 2

**It's been 15 years since the Crucible failed and the Catalyst decided to exterminate the galaxy. In that time the Resistance has spread and fought back, but now the Reapers attacks are only more savage as they near their ultimate goal. As the leaders of the war grow desperate, some look to Commander Shepard for direction, believing him to be a savior who will lead them to victory. Others see him as a false hope. But Shepard himself is starting to lose faith...**

The squad of shuttles approached their target, a Reaper base on a hot desert planet. Intel suggested this was a Research and Development Lab, or the Reaper equivalent of one. A group of fighters was escorting the shuttles, a target like this was going to be well defended. As they approached, an array of alien-looking satellite dishes came into view. A Reaper Destroyer was guarding the array and immediately noticed the convoy approaching. One of the fighters was shot out of the sky. Another fired a massive Thanix missile at it. The Destroyer and several dishes were taken out, leaving a crater in its place. The other fighters started attacking the remaining dishes while the shuttles all landed on the ground. A human soldier stepped out of the shuttle and fired at a few Cannibals that had been waiting.

"This is Shepard" he said "We're on the ground"

"Roger that, Shepard" replied Major Colsen. "Rendezvous on my position, we need to get inside!"

"We'll be there" Shepard and his squad, all human for this mission, started fighting their way through, his omni-tool telling him where the Major was. They took fire from all sides from Cannibals, Ravagers, Marauders, and Geth bodies filled with Reaper code which had since come to be labelled "Infected Geth". The fighters were now engaged in a dogfight with Oculus drones above them, occasionally they had to dodge falling wreckage.

"Commander, how are we getting in?" one of his men asked

"Lets just focus on getting there first, private!" Shepard shouted back, shooting a Ravager as he did so. He saw several shuttles destroyed before they could unload their soldiers, he saw a squad of turians vaporized by a passing Oculus.

"Move it, people, now! We're almost there!" He checked his omni-tool. They were coming up to Colsen now. They found him by a large sealed doorway.

"Shepard, glad you could make it, we were starting to get worried" he joked

"Well I didnt want to show up too early..." he joked back

"We're just waiting on the demo guys, they're a squad of krogan, so you know they pack a punch. Ah, here they come now." He said as they fought off some husks. Shepard saw five krogan running towards them, from the look of them they were loving this battle.

"Ha Ha Ha! Alright you girls move up! Drakk, get the good stuff out and take down this ugly looking door!" shouted what Shepard assumed was the leader of the group.

"Major, Urdnot Brenn" he said, identifying himself. "I heard you ordered some krogan locksmiths?" he nodded with a grin towards Drakk, who was carrying a heavy looking explosive.

"Affirmative, get that thing on the door before reinforcements show up" Colsen said as Drakk places the ordnace on the door.

"Right everyone back, now!" Drakk shouted, arming the device. They all ran towards some wreckage, but a banshee appeared and started throwing biotics at them, taking out some of Shepards squad. Shepard jumped out of the way, hitting the floor. He turned around so he was in a sitting-up position and started spraying the Banshee with bullets

"Drakk, how long till that bomb goes off?!" he yelled, looking for the krogan

"Seconds! Get to cover, I got this!" he shouted back, Shepard saw he was still protecting the bomb. Shepard didnt like the sound of that, but got to his feet and sprinted for the wreckage, doing a full vault over and joining his squad, Colsen and his squad, and Brenn and his squad. They all leaned over and at once started shooting at the Banshee. Which wasnt doing much good.

"Come here, asari bitch! you're mine!" Drakk shouted, he ran to the Banshee and full-on picked her up off the ground. The Banshee was screaming and thrashing around, scratching and cutting at Drakk, who only shouted and screamed back. He managed to carry her back to the bomb on the door and yell one last war-cry before it detonated, taking them both out, along with the door. As they all got up from cover, Colsen was the first to speak.

"Right, everyone inside, theres still a war going on out here!" He led the others in.

Shepard walked past Brenn. "Drakk was a good man, he saved us all." he said to the krogan

"He proved himself worthy of bearing the name of Urdnot, and brought honor to his clan and child" Brenn replied, with no hint of sadness in his voice, only admiration.

"Shepard! take point!" Colsen ordered

"Yes Sir. Malcolm, Fred" Shepard addressed the two remaining members of his squad "take up the rear, make sure nothing sneaks up on in here"

"Yes Sir" they both said. Shepard went ahead of Colsen inside the bunker.

"So Major Colsen, what are we looking for in here?" Shepard asked

"Info is need-to-know only Shepard, suffice to say this mission has been given a Priority One designation."

"Well since we're here, you may as well tell me now" Shepard pressed the issue.

"Shepard, lets get one thing clear, _I _am in command of this mission, not you. I have the greatest respect for you and your reputation, but dont think that your above me because your a Spectre. Since the Citadel belongs to the Reapers now and the Council has absolutely no power anymore, your Spectre status doesnt mean shit to me or anyone else in the galaxy. The Council doesnt exist, its just us and the Reapers.

Shepard didnt like Colsen much

They carried on through the facility, encountering resistance along the way. Eventually they came to what looked like a control room.

"Santos, your up. do your thing" Colsen ordered the tech expert in his squad. Santos started hacking into the Reaper computers and bringing files up. "What have you got?" Colsen asked.

"Sir, there are hundreds of prisoners here!" he said "Some of every race, turian, asari, salarians, volus, everyone. But eighty-three percent of them are human"

"This place is a research lab, sick fuckers" Colsen said "send the data to Command"

"Wait, Santos, go back" Shepard said, he had been looking over Santos's shoulder at the Reaper files, "what are they using all those humans for?" he said, dreading the answer.

"All the aliens and a small minority of the humans are being used for experimentation" Santos explained, "but all the other humans are being moved Reaper Central, for some new project."

"Earth" Shepard said. Since they had abandoned humanity's homeworld to the Reapers, Earth had no longer been seen as belonging to humanity or even worth saving. The whole planet was in ruins, the cities were burnt to the ground, and the Citadel still hung over Earth, in the very heart of the Reapers territory. No allied ships had passed through the Sol Relay in over a decade. The Resistance had since named the whole system as "Reaper Central".

"Whats this project then, Santos?" Shepard asked.

"One sec, just bringing it up on screen now" he pressed a few buttons. An image appeared on the screen. First a human, which then turned into an image of a double-helix, human DNA. Then it changed again into a machine. A human-shaped machine.

"A human Reaper" Malcolm said, shocked. He looked at Shepard "Its just like you said, exactly the same"

"No, its worse" Shepard said back "this ones nearly finished."

"Shepard, get out of all that, need-to-know!" Colsen ordered "we send this to cammand, Shepard, get back topside, Bravo teams not responding. Make sure our exit strategy is good to go."

Shepard found his way back to the surface, the fighters were gone, as were the Oculi. Shepard assumed the Oculi had won the dogfight and bugged out.

"Bravo Team, come in" Shepard tried "Bravo Team are you up here? Respond" Nothing. "Colsen, Bravo's not responding, assumed dead. Theres still a shuttle up here. I'll prep it for launch."

"Roger that, Shepard. I'm sending Brenn and his boys back up to mind the shuttle with you, in case we're not alone. Me and the men down here will wait for the data to send and we'll join you." Several minutes passed and the four krogan appeared.

"Shepard, hows things?" Brenn asked

"I'm no expert on shuttles, but... err... good" he said, giving a thumbs-up. Then Colsens voice came over the radio

"Aghh! Shepard! Data's been sent, but they know we've done something. Heavy resistance. We're making our way back up. Watch yourself, they may be coming for you!"

Shepard looked at the krogan, "Right boys, we're about to get hit, when that happens we-" a Brute came out of nowhere and impaled one of Brenns men with its massive claw arm, throwing away the body like it was a rag doll. Shepard and the krogan set about taking it out straight away, the Brute killed another krogan, before taking on Brenn. An infected geth Prime appeared and killed Brenns other squad member, leaving just Brenn and Shepard fighting them. Shepard threw a grenade at the prime, blowing it into two pieces, then went to help Brenn.

"Come on then you bastard, finish me off!" Brenn yelled at the Brute, fighting it head on and losing fast. Shepard saw the heavy machine gun mounted on the evac shuttle and took control of it. Then he emptied the gun on the Brute, eventually bringing it down.

"Well, that was fun" Brenn said, he looked at Shepard, "thanks"

Shepard was about to reply when a massive explosion went off. It must have come from underground, the whole facility went up in flames, the shockwave knocking them both to their feet.

"Colson?" Shepard asked into his radio, getting back to his feet. "Colson!" No reply.

"Dead" Brenn said. "Come on, lets get out- " as he said that, the top half of the geth prime Shepard had just blown up climbed onto Brenns shoulders with one of the other krogans heavy shotguns, Brenn realized what was going on too late before the prime blew his head off.

"No!" Shepard shouted as the prime fell to the floor with Brenns body. It went for the shotgun again and shot at Shepard just as he jumped out the way. The shotgun was empty now and useless. The prime climbed onto Shepard, who was still on the floor, and tried to smash his head in. Shepard punched it in the face before crying out in pain, the geth was made of metal. He managed to shove it off and looked around for a weapon. He saw a large piece of metal with some rubble attached sticking out of some wreckage. Grabbing this makeshift club he waited for the machine to crawl towards him, as it came close he took a swing, knocking it on its back. While it was disorientated Shepard swung down on its face, smashing its red eye-pieces. He kept swinging at the face until he was sure it was dead. After he was sure, he sat down for a moment to catch his breath. He was the only survivor. All he could do now was leave. He got up and walked into the shuttle. He tried one more time for survivors.

"This is Commander Shepard, are there any survivors? Repeat: are there any survivors?" no one.

Sighing, he lifted off. Looking out at the sunset, he plotted a course off planet and set off back home.


	3. Chapter 3

Shepards shuttle headed out of the planets atmosphere, he put it into auto pilot to head into FTL outside the system, all he could do now was wait until it took him home. He wondered what was so important about that data. He sat back and tried to rest while the shuttle carried on. The war had taken its toll on the rest of the galaxy. Since the Crucible had failed and the Catalyst had turned homicidal, the Reapers had devastated every colonised world in the galaxy, this had been merely so that organic races couldnt regroup and plan. many people still lived on some of these post-apocalyptic worlds, cut of from the galaxy and fighting each other for scraps. The Reapers would most likely return and wipe these scroungers out once their war was won. Right now their priority was destroying the Resistance. The Resistance was spread out across many worlds and bases, some even hiding in the ruins of worlds the Reapers had ravaged. The Resistance leaders were hidden on a single command ship, which was constantly on the move so as not to be found. They included the military leaders of all the races involved in the war. Admiral Hackett leading humanity, Primarch Victus for the turians, Urdnot Wrex leading the krogan, Balak - who had put his grudge against humans behind him- leading the batarians, major Kirahe had since taken control of the salarian forces after the dalatrass lost power, an asari names Matriarch Adora lead the asari forces, the quarians were organised by Admiral Han'Gerrel and the geth had assigned a geth unit to speak for them amongst the other leaders, none of the other races were strong enough and had to fight with the rest. Shepard was in charge of his own Resistance Cell which was based on Omega. Aria still controlled the station but Shepard was given free reign to do as he pleased and whatever he thought was necessary.  
After several hours in the shuttle he came out of FTL and could see Omega growing closer.

"Omega Control, this is Shepard, requesting entry" he said over the comm.

"Please verify" he heard a woman reply.

"No matter if I am the Alpha of my men, I will always return here, to the Omega of the stars" he said. Each departure from the station was given a phrase to tell upon arrival, a technique borrowed from the quarians. He wondered who had chose that one for him

"Welcome home, Commander. Proceed to the hangar. Wheres everyone else, sir?" She asked

"They didnt make it" he replied. The woman on the other end didnt say anything else. Shepard landed the shuttle in one of the landing bays. He got out and made his way to one of the transports that would take him to the command center. As he looked out the windows he could see a few shuttles and gunships flying around, transporting stuff around the station. Since Shepard had taken over the station, Omega had become a military zone, a state which the residents seemed almost happy about. Shepard arrived and got out of the transport, as he walked past numerous soldiers they all stopped to salute him. They had all probably heard about the assault on the Reaper base. He rounded a corner and saw his old friend staring at him.

"Shepard, you old bastard, whats this I hear about you invading Reaper bases and not taking your favourite turian with you?" Garrus Vakarian joked.

"Just as well you didnt come, Garrus, I was the only survivor" Shepard said

"I know, word spreads quick, lets just hope it was worth it. On another note, theres someone who wants to see you" he said with what Shepard could only guess was a turian grin. Shepard continues on down the hallway until he saw an asari monitering a computer. She looked up at him.

"Shepard" she said with a smile.

"Liara" he said back, running towards her, giving her a big hug.

"I thought you were dead!" she said

"It takes more than death to kill me, remember?" he said with a smirk.

"You say that so casually, but what if it was you who died at that base?"

"Liara listen to me, you crazy woman" he said, looking in her eyes, "Im not going to die, Ive only just got back after all, imagine how _stressed _I am..." he said with a grin.

"Fine, I'm sorry, and I think we can fix that..." she grinned back.

"Good, but I have to talk to Command first, figure out what was so important about that base"

"They didnt tell you when you went in?" Liara asked, puzzled.

"Nope, Im gonna talk to them now" Shepard went into a room to change from armour into regualr clothes, slinging on some boots, trousers, shirt and a plain green jacket before heading into Omega's command room. EDI was inside monitering several computers.

"Shepard, how was your previous mission?" she asked

"Terrible, EDI, I thought you would have heard I was the only one to make it?"

"I did, but wished to hear you personal opinion"

"Nice, well I need to speak to Command, patch me in through the QEC"

"Roger that" she said as he stepped into the comm room.

* * *

_**Resistance Command Headquarters**_

_**Alliance Dreadnought Kilimanjaro:**_

Admiral Hackett stepped into the ships comm room with the other alien leaders, he'd read in the mission report that Shepard was the only survivor. Hackett guess that Shepard would want answers, and thought that was perfectly understandable. Shepards blue image appeared on the holgraphic projector

"Commander Shepard" Hackett said, "I heard what went down at that base, Im sorry no one else made it. I imagine your looking for answers."

"What did we find down there?" he cut to the chase.

"We found the answer, Shepard. A way to beat these bastards once and for all!" Wrex piped in.

"As you know, Commander Shepard," Primarch Victus said, "The Reapers all communicate with each other simultaneously through the catalyst and the Citadel. The Reapers collective memories and minds add to the Catalysts intelligence, and it in turn controls the Reapers. While they can survive on theyre own, they are always linked to each other. We learned of this link when the Crucible was connected to the Citadel. While it didnt work, it did give us information on the Catalyst and its network with the Reapers."

"We found a way to exploit this link" Kirahe started "its taken years of searching but we finally found it: a control signal hidden right in the base codes of the Reapers."

"We believe this is what the Illusive Man was looking for all those years ago, he might have even found it before he died." Hackett explained "We dont know how to control the Reapers directly, Cerberus were the only ones who figured that one out. But this control signal will allow us to hijack the Reaper network and destroy it, taking them and the Catalyst with it."

"Grab the Reapers by their throats and slit them" Wrex said, dragging a finger along his own.

"In a sense, yes" Hackett said.

"Does it work?" Shepard asked, wanting to know more.

"We believe the code is genuine and that it will work on all the Reapers, we still have to test it in the field though." Matriarch Adora spoke up.

"Give me the code" Shepard told them, "I'll do it."

"Hold on now, Shepard" Balak spoke out this time, "This isnt just some new toy for you to go throwing at a random Reaper ship! If the Reapers find out about this, we'll all pay the price. I'll be damned if I let the Reapers discover this because of _you_." Shepard tried not to tell the batarian to piss off. While Balak had cooperated fully with humans and done nothing to jeopardize their chances in the war, he had never fully forgiven Shepard for destroying the Bahak System. He knew it had been to delay the Reapers, but that just made it worse, knowing there was a good reason for doing it.

"Shut the hell up, Balak." Wrex told him, "If anything, Shepards the best choice for something like this." Balak didnt say anything.

"So if this code works, what then?" Shepard asked.

This time it was the geth that spoke, "We believe that the Reaper Code must be directly uploaded to the centre of the Reaper Network, and interface with the Catalyst itself."

"Reaper Central" Shepard said, "the Citadel."

"Exactly" Hackett replied

"Give me the code" Shepard repeated "We'll field test it and get back to you with the results"

"Good man" Hackett smiled. His face turned serious and he looked a bit older for a moment, almost tired, "Shepard if we do this right, then the war is over. No more fighting, no more running. You've seen the intercepted transmissions. Everyone in this room is on the Reapers priority kill-list, including you."

"I understand Sir." Shepard knew he was on the Reaper hit-list. In fact, he was number one.

"We'll send you the code. Good luck, Commander. Kilimanjaro out" Hackett said before cutting the transmission.

Shepard thought for a moment about everything they had just talked about. A Reaper kill-switch? he thought it was too good to be true, and also a bit of a dues ex machina. But then he realised that he wasnt going to be choosey about a weapon that could kill the Reapers, no matter how cliched it was. He went back into the control room, there was a lot of work to be done.


End file.
